Basically - your document is very complex in terms of how it's put together in the background.

If you print to PDF you lose a lot that complex goodness that is information used by printing presses, and in Adobe reader.

Printing to a PDF file causes all sorts of complex things to be stripped to it's bare bones. Like Transparency is not retained. Instead the image is broken up into simpler pieces and stitched back together.

On behalf of Adobe, confirm that export to PDF/X-4 (there is not PDF/X-4a) is the method that yields the most reliable PDF publishing workflow, especially if you need to print or even re-purpose the content.